Root microbiome response to treated wastewater irrigation

Rhizosphere microbiome influence on tomato growth under low-nutrient settings

Studies have suggested that reduced nutrient availability enhances microbial diversity around plant roots, positively impacting plant productivity. However, the specific contributions of rhizosphere microbiomes in nutrient-poor environments still need to be better understood. This study investigates tomato (Solanum lycopersicum L.) root microbiome under low-nutrient conditions. Plants were grown in hydroponics with soil-derived microbial community inoculations. We hypothesized that nutrient limitation would increase the selection of beneficial bacterial communities, compensating for nutrient deficiencies. We identified 12 294 operational taxonomic units across treatments and controls using 16S rRNA gene sequencing. Increased plant biomass was observed in treatments compared to controls, suggesting a role for the microbiome in mitigating nutrient limitations. The relative abundance of genera such as Luteolibacter and Sphingopyxis relative abundance correlated with plant phenotypic traits (P ≤ .05), and their presence was further validated using shotgun metagenomics. We annotated 722 677 protein families and calculated a core set of 48 116 protein families shared across all treatments and assigned them into bacteria (93.7%) and eukaryota (6.2%). Within the core bacterial metagenome, we identified protein families associated with pathways involved in positive plant interactions like the nitrogen fixation. Limited nutrient availability enhanced plant productivity under controlled conditions, offering a path to reduce fertilizer use in agriculture.

Seasonal dynamics and functional diversity of soil nematode communities under treated wastewater irrigation in abandoned agricultural soils

The use of treated wastewater (TWW) for agricultural irrigation is becoming more popular as a sustainable alternative to freshwater due to increasing water scarcity. While considerable research exists on the effects of TWW on soil microorganisms, its impact on soil nematodes, key indicators of soil health remains unexplored. This study assessed the effects of two years of TWW irrigation on soil nematode communities in abandoned fields cultivated with Lavender, Anise, Olive and Pomegranate trees. Seasonal soil samples were analyzed for nematode abundance, community composition and ecological indices. TWW irrigation modified soil nematode community structure, favoring the dominance of bacterivores (Acrobeloides) while suppressing plant-parasitic nematodes (Pratylenchus, Bitylenchus). Nematode-based indices showed no significant differences between TWW- and freshwater-irrigated soils, indicating stable and resilient communities. Seasonal precipitation levels strongly influenced nematode abundances, highlighting environmental resilience. Plant species did not create ecological niches, probably due to the strong influence of precipitation and soil properties; nevertheless, plant establishment increased nematode diversity over time, with omnivores and predators emerging alongside bacterivores and fungivores, reflecting recovery dynamics. Even though TWW irrigation is considered a type of disturbance, it facilitated soil nematode diversity and maintained ecological stability. Properly treated wastewater serves as a sustainable irrigation method that enhances soil health and biodiversity, rendering it a viable alternative for agricultural systems in degraded and water-scarce areas under changing climatic conditions.

Impacts of long-term irrigation of municipally-treated wastewater to the soil microbial and nutrient properties

Reusing treated wastewater (TWW) for crop irrigation has shown to provide environmental and economic benefits as well as drawbacks. This study was conducted using soils collected from a wastewater reuse facility in Tallahassee, FL, mainly to elucidate the long-term impact(s) of TWW irrigation on soil microbiome and nutrient status. Approximately 890 ha of land have been spray-irrigated with TWW since the 1980's to grow fodder crops. Soil cores were collected from six irrigated and six control sites at depths of 0-15, 15-30, and 30-60 cm during summer and winter, followed by nutrient analysis and assessment of bacterial, fungal, and denitrifier communities using SSU rRNA, ITS, nirK, nirS, and nosZ phylogenetic markers. TWW irrigation significantly increased soil pH, soluble salts, nitrate, phosphate, calcium, magnesium, and organic matter, alongside shifts in the prokaryotic and fungal community structures, particularly in summer. Beta-diversity analyses indicated that wastewater quality and season collectively explained 23 % of prokaryotic community similarity and 9.8 % of fungal community dissimilarity. Indicator species analysis, supported by random forest machine learning, identified 37 prokaryotic and 11 fungal bioindicators whose occurrences varied significantly with wastewater quality and season. Key nitrogen-cycling microbes included ammonia-oxidizing families of Nitrosomonadaceae, Nitrosopumilaceae, Nitrososphaeraceae, Nitrosotaleaceae, and comammox-performing Nitrospiraceae. The fungal community was predominated by Ascomycota (78.6 % ± 4.2 %). FUNGuild analysis showed dominant trophic levels of symbiotrophs, saprotrophs, and pathotrophs, averaging 42 % ± 7.1 %. Overall, this study points to the long-term impacts of TWW irrigation on the studied soil properties and microbial communities.

Risk characterisation of chemicals of emerging concern in real-life water reuse applications

Water reuse is a viable option to address temporal or structural water shortages. However, the ubiquitous presence of chemicals of emerging concern (CECs) in natural systems, especially the aquatic environment, represents a significant obstacle to water reuse and the receiving environment. Therefore, an extensive literature review was performed to identify current water reuse practices at field scale, reported types and levels of CECs and their associated risks for human and environmental health. Treated wastewater was the primary reused water source, with agricultural reuse being the most frequently reported reuse application (28 %), followed by indirect-potable reuse (16 %). Contrary to potable reuse, it was observed that almost no studies applied additional treatment before water reuse for agricultural purposes. Based on calculated risk quotients, ecological risks were identified for perfluorooctanesulfonic acid, chlorpyrifos, triclocarban, and ethinylestradiol, and human health risks for perfluorooctanesulfonic acid and perfluorooctanoic acid. Environmental risks could be assessed for 77 % of detected CECs, while the human health risk assessment is limited to 28 %. For agricultural reuse, it was observed that CEC concentrations in produced crops were at acceptable levels. However, a thorough risk assessment of CECs during water reuse is currently limited due to a focus on a defined class of contaminants in the literature, i.e., pharmaceuticals, and falls short of per- and polyfluoroalkyl substances. Therefore, future water reuse studies should include a broader set of CECs and study additional mitigation options to decrease CEC concentrations before or during water reuse. Moreover, environmental harm caused by CECs during water reuse such as adverse effects on the microbial soil community or leaching to non-target sources has hardly been studied in the field and presents a knowledge gap.

Short-term effect of reclaimed water irrigation on soil health, plant growth and the composition of soil microbial communities

The scarcity of freshwater poses significant challenges to agriculture, often necessitating the use of alternative water sources such as reclaimed water. While reclaimed water offers a viable solution by providing water and nutrients to crops, its potential impacts on soil microbial communities remain a subject of investigation. In this investigation, we conducted a field experiment cultivating Maize (Zea mays) and Lavender (Lavandula angustifolia), employing irrigation with reclaimed water originating from domestic wastewater, while control samples were irrigated using freshwater. Utilizing high-throughput sequencing, we assessed the effect of reclaimed water on soil bacteria and fungi. Plant biomass exhibited a significant response to treated wastewater. Alpha diversity metrics of soil microbial communities did not reveal significant changes in soils irrigated with reclaimed water compared to control samples. Reclaimed water, however, demonstrated a selective influence on microorganisms associated with nutrient cycling. Co-occurrence network analysis unveiled that reclaimed water may alter soil microbial community structure and stability. Although our work presents overall positive outcomes, further investigation into the long-term implications of reclaimed water irrigation is warranted.

Embracing complexities in agricultural water management through nexus planning

A major challenge for agricultural water management (AWM) in the 21st century is to feed a growing population in the face of increasing intersectoral resource competition, evolving diets, degradation, pandemics, geopolitical conflicts and climate change. This has to be achieved within the planetary boundaries and without compromising the livelihood and environmental (ecosystem) objectives linked to water, including provisioning, supporting and regulating services. This paper uses a systems and nexus lens to unravel the centrality and complexities in AWM, with particular emphasis on the interconnected dimensions and objectives of AWM, as well as its practices and technologies. AWM exists beyond water and food with linkages to human and environmental well-being. AWM needs to catalyse transformation and integrate approaches across systems, users and scales to meet its objectives in a changing climate. It must provide perspectives beyond productivity, managing water risks and safeguarding food security - as important as these are - and integrate our understanding of the interconnected climate, land, water, food and ecosystems to address planetary health outcomes. By doing so, AWM could catalyse contextualised, equitable, innovative solutions that acknowledge local socio-economic and institutional structures and limitations while catalysing sustainable development and climate resilience.

Balancing the scales: assessing the impact of irrigation and pathogen burden on potato blackleg disease and soil microbial communities

BACKGROUND

Understanding the interaction between environmental conditions, crop yields, and soil health is crucial for sustainable agriculture in a changing climate. Management practices to limit disease are a balancing act. For example, in potato production, dry conditions favour common scab (Streptomyces spp.) and wet conditions favour blackleg disease (Pectobacterium spp.). The exact mechanisms involved and how these link to changes in the soil microbiome are unclear. Our objectives were to test how irrigation management and bacterial pathogen load in potato seed stocks impact: (i) crop yields; (ii) disease development (blackleg or common scab); and (iii) soil microbial community dynamics.

METHODS

We used stocks of seed potatoes with varying natural levels of Pectobacterium (Jelly [high load], Jelly [low load] and Estima [Zero - no Pectobacterium]). Stocks were grown under four irrigation regimes that differed in the timing and level of watering. The soil microbial communities were profiled using amplicon sequencing at 50% plant emergence and at harvest. Generalised linear latent variable models and an annotation-free mathematical framework approach (ensemble quotient analysis) were then used to show the interacting microbes with irrigation regime and Pectobacterium pathogen levels.

RESULTS

Irrigation increased blackleg symptoms in the plots planted with stocks with low and high levels of Pectobacterium (22-34%) but not in the zero stock (2-6%). However, withholding irrigation increased common scab symptoms (2-5%) and reduced crop yields. Irrigation did not impact the composition of the soil microbiome, but planting stock with a high Pectobacterium burden resulted in an increased abundance of Planctomycetota, Anaerolinea and Acidobacteria species within the microbiome. Ensemble quotient analysis highlighted the Anaerolinea taxa were highly associated with high levels of Pectobacterium in the seed stock and blackleg symptoms in the field.

CONCLUSIONS

We conclude that planting seed stocks with a high Pectobacterium burden alters the abundance of specific microbial species within the soil microbiome and suggest that managing pathogen load in seed stocks could substantially affect soil communities, affecting crop health and productivity. Video Abstract.

Removal of intracellular and extracellular antibiotic resistance genes and virulence factor genes using electricity-intensified constructed wetlands

Constructed wetland (CW) is considered a promising technology for the removal of emerging contaminants. However, its removal performance for antibiotic resistance genes (ARGs) is not efficient and influence of virulence factor genes (VFGs) have not been elucidated. Here, removal of intracellular and extracellular ARGs as well as VFGs by electricity-intensified CWs was comprehensively evaluated. The two electrolysis-intensified CWs can improve the removal of intracellular ARGs and MGEs to 0.96- and 0.85-logs, respectively. But cell-free extracellular ARGs (CF-eARGs) were significantly enriched with 1.8-logs in the electrolysis-intensified CW. Interestingly, adding Fe-C microelectrolysis to the electrolysis-intensified CW is conducive to the reduction of CF-eARGs. However, the detected number and relative abundances of intracellular and extracellular VFGs were increased in all of the three CWs. The biofilms attached onto the substrates and rhizosphere are also hotspots of both intracellular and particle-associated extracellular ARGs and VFGs. Structural equation models and correlation analysis indicated that ARGs and VFGs were significantly cooccurred, suggesting that VFGs may affect the dynamics of ARGs. The phenotypes of VFGs, such as biofilm, may act as protective matrix for ARGs, hindering the removal of resistance genes. Our results provide novel insights into the ecological remediation technologies to enhance the removal of ARGs.

Mitigating risks and maximizing sustainability of treated wastewater reuse for irrigation

Scarcity of freshwater for agriculture has led to increased utilization of treated wastewater (TWW), establishing it as a significant and reliable source of irrigation water. However, years of research indicate that if not managed adequately, TWW may deleteriously affect soil functioning and plant productivity, and pose a hazard to human and environmental health. This review leverages the experience of researchers, stakeholders, and policymakers from Israel, the United-States, and Europe to present a holistic, multidisciplinary perspective on maximizing the benefits from municipal TWW use for irrigation. We specifically draw on the extensive knowledge gained in Israel, a world leader in agricultural TWW implementation. The first two sections of the work set the foundation for understanding current challenges involved with the use of TWW, detailing known and emerging agronomic and environmental issues (such as salinity and phytotoxicity) and public health risks (such as contaminants of emerging concern and pathogens). The work then presents solutions to address these challenges, including technological and agronomic management-based solutions as well as source control policies. The concluding section presents suggestions for the path forward, emphasizing the importance of improving links between research and policy, and better outreach to the public and agricultural practitioners. We use this platform as a call for action, to form a global harmonized data system that will centralize scientific findings on agronomic, environmental and public health effects of TWW irrigation. Insights from such global collaboration will help to mitigate risks, and facilitate more sustainable use of TWW for food production in the future.

Impact of Aerated Drip Irrigation and Nitrogen Application on Soil Properties, Soil Bacterial Communities and Agronomic Traits of Cucumber in a Greenhouse System

Root hypoxia stress and soil nutrient turnover have been related to reduced crop productivity. Aerated drip irrigation (ADI) can effectively enhance crop productivity and yield. However, the response of the soil bacterial community to different irrigation water dissolved oxygen (DO) concentrations remains elusive due to the extreme sensitivity of microorganisms to environmental variations. We investigated the effects of aerated irrigation with different concentrations of DO on soil properties and agronomic performance of cucumber, as well as the contribution of the bacterial community. We performed experiments on cucumber cultivation in Shouguang, China, including different irrigation methods (ADI: O2-10 and O3-20 mg L-1, non-aerated groundwater: O1-5 mg L-1) and nitrogen (N) application rates: 240 and 360 kg N ha-1. ADI (particularly O2) significantly improved soil properties, root growth, cucumber yields, and irrigation water use efficiency (IWUE), and appropriate DO concentrations reduced N fertilizer application and increased crop yields. Furthermore, these changes were associated with bacterial community diversity, aerobic bacteria abundance, and consolidated bacterial population stability within the network module. Environmental factors such as soil respiration rate (Rs), DO, and NO3--N have significant effects on bacterial communities. The FAPROTAX results demonstrated enhanced nitrification (Nitrospira) and aerobic nitrite oxidation by soil bacteria under ADI, promoting the accumulation of effective soil N and improved soil fertility and crop yield. Appropriate DO concentration is conducive to the involvement of soil bacterial communities in regulating soil properties and cucumber growth performance, which are vital for the sustainable development of facility agriculture.

Effect of long-term influx of tertiary treated wastewater on native bacterial communities in a dry valley topsoil: 16S rRNA gene-based metagenomic analysis of composition and functional profile

Although dumping treated wastewater into soil might provide nutrients and organic matter, it can also expose the ecosystem to biological and chemical risks. A vital indication of soil health and quality is the soil microbial community. The current work used next-generation 16S rRNA gene amplicon sequencing to evaluate the effects of the long-term influx of tertiary treated wastewater (TWW) into Wadi Uranah, a dry valley in Makkah city, Saudi Arabia, on native topsoil bacterial community composition and predicted functions. The findings demonstrated that neither the compositions of microbial communities nor their predicted functions using PICRUSt2 differed significantly (p > 0.05) between polluted valley soil (PolVS) and unpolluted valley soil (UPVS). Alpha and beta diversity, however, showed that the PolVS samples had a considerably higher level of diversity and variability. Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes were the most prevalent phyla in both groups. Noticeable relative variations existed in some metabolic pathways such as cofactor, prosthetic group, electron carrier degradation, aldehyde degradation, and Entner-Doudoroff (ED) pathways. Overall, our findings suggest that because both groups have very similar core microbiomes and functions, the long-term disposal of tertiary TWW into Wadi Uranah may have little to no influence on the composition and function of soil bacterial communities. In addition, the long-term discharge of tertiary TWW after partially treated wastewater's initial disposal may have helped the native soil microbial community recover.

Short- and long-term effects of continuous compost amendment on soil microbiome community

Organic amendment, and especially the use of composts, is a well-accepted sustainable agricultural practice. Compost increases soil carbon and microbial biomass, changes enzymatic activity, and enriches soil carbon and nitrogen stocks. However, relatively little is known about the immediate and long-term temporal dynamics of agricultural soil microbial communities following repeated compost applications. Our study was conducted at two field sites: Newe Ya'ar (NY, Mediterranean climate) and Gilat (G, semi-arid climate), both managed organically over 4 years under either conventional fertilization (0, zero compost) or three levels of compost amendment (20, 40 and 60 m3/ha or 2, 4, 6 L/m2). Microbial community dynamics in the soils was examined by high- and low-time-resolution analyses. Annual community composition in compost-amended soils was significantly affected by compost amendment levels in G (first, second and third years) and in NY (third year). Repeated sampling at high resolution (9-10 times over 1 year) showed that at both sites, compost application initially induced a strong shift in microbial communities, lasting for up to 1 month, followed by a milder response. Compost application significantly elevated alpha diversity at both sites, but differed in the compost-dose correlation effect. We demonstrate higher abundance of taxa putatively involved in organic decomposition and characterized compost-related indicator taxa and a compost-derived core microbiome at both sites. Overall, this study describes temporal changes in the ecology of soil microbiomes in response to compost vs. conventional fertilization.

Application Effect of MF-OP on Collection of Trivalent Holmium from Rare Earth Mining Wastewater

Microtube microfilter with organic phosphoric acid (expressed as MF-OP) containing a wastewater portion with buffer fluid and an enriched portion with nitric acid fluid and organic phosphoric extractant dissolved in benzin has been studied for its trivalent holmium (expressed as Ho(III) collection from rare earth wastewater. Common parameters affecting the collection effect have been investigated, including hydrogen ion molar concentration (molar concentration can be expressed as Cm) or pH value, initial concentration (expressed as Co) of Ho(III), ion-force of rare earth wastewater, voluminal proportion of organic phosphoric extractant with benzin and nitric acid fluid (expressed as Vr), nitric acid Cm, extractant Cm, and type of acid fluid in an enriched portion. The virtues of MF-OP compared to the traditional collection was explored. The impacts of hydrodynamic characteristics (steadiness and current speed) and MF parameter factors (inradius of tube, tube-shell thickness, proportion of holes) on the collection performance of MF-OP for Ho(III) collection were also considered. The test results displayed that the greatest collection conditions of Ho(III) were attained as nitric acid Cm was 4.00 mol/L, extractant Cm was 0.220 mol/L, and Vr was 0.8 in the enriched portion, and pH value was 4.60 in the wastewater portion. Ion- force of rare earth wastewater had no noticeable outcome on Ho(III) collection. The collection proportion of Ho(III) was attainable to 93.1% in 280 min, while Co was 1.80 × 10-3 mol/L.

Fate and impact of wastewater-borne micropollutants in lettuce and the root-associated bacteria

The reuse of water for agricultural practices becomes progressively more important due to increasing demands for a transition to a circular economy. Treated wastewater can be an alternative option of blue water used for the irrigation of crops but its risks need to be evaluated. This study assesses the uptake and metabolization of pharmaceuticals and personal care products (PPCPs) derived from treated wastewater into lettuce as well as the impact on root-associated bacteria under a realistic and worst-case scenario. Lettuce was grown in a controlled greenhouse and irrigated with water or treated wastewater spiked with and without a mixture of fourteen different PPCPs at 10 μg/L or 100 μg/L. After harvesting the plants, the same soil was reused for a consecutive cultivation campaign to test for the accumulation of PPCPs. Twelve out of fourteen spiked PPCPs were detected in lettuce roots, and thirteen in leaves. In roots, highest concentrations were measured for sucralose, sulfamethoxazole and citalopram, while sucralose, acesulfame and carbamazepine were the highest in leaves. Higher PPCP concentrations were found in lettuce roots irrigated with spiked treated wastewater than in those irrigated with spiked water. The absolute bacterial abundance remained stable over both cultivation campaigns and was not affected by any of the treatments (type of irrigation water (water vs. wastewater) nor concentration of PPCPs). However, the irrigation of lettuce with treated wastewater had a significant effect on the microbial α-diversity indices at the end of the second cultivation campaign, and modified the structure and community composition of root-associated bacteria at the end of both campaigns. Five and fourteen bacterial families were shown to be responsible for the observed changes at the end of the first and second cultivation campaign, respectively. Relative abundance of Haliangium and the clade Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium was significantly affected in response to PCPPs exposure. Caulobacter, Cellvibrio, Hydrogenophaga and Rhizobacter were significantly affected in microcosms irrigated with wastewater.

Non-target and suspect-screening analyses of hydroponic soybeans and passive samplers exposed to different watershed irrigation sources

Water scarcity increases the likelihood of irrigating food crops with municipal wastewater that may pose potential dietary risks of regulated and non-regulated organic chemical uptake to edible plant tissues. Only a few studies have used high resolution mass spectrometry (HRMS) to assess the uptake of chemicals of concern into food crops. This study used non-target and suspect-screening analyses to compare total chemical features, tentatively identified chemicals (TICs), and EPA ToxCast chemicals in soybean plants and passive samplers exposed to five different irrigation sources that were collected from an agricultural watershed during mild drought conditions. Secondary-treated municipal wastewater effluent, two surface waters, two ground waters, and deionized municipal tap water were used for two hydroponic experiments: soybean roots and shoots and Composite Integrative Passive Samplers (CIPS) harvested after fourteen days of exposure and soybeans after fifty-six days. CIPS were sealed in separate glass amber jars to evaluate their efficacy to mimic chemical features, TICs, and ToxCast chemical uptake in plant roots, shoots, and beans. Total soybean biomass and water use were greatest for tap water, municipal wastewater, and surface water downstream of the municipal wastewater facility relative to groundwater samples and surface water collected upstream of the wastewater facility. ToxCast chemicals were ubiquitous across watershed irrigation sources in abundance, chemical use category, and number. Wastewater-exposed soybeans had the fewest extractable TICs in plant tissues of all irrigation sources. More ToxCast chemicals were identified in CIPS than extracted from irrigation sources by solid phase extraction. ToxCast chemicals in beans and CIPS were similar in number, chemical use category, and log Kow range. CIPS appear to serve as a useful surrogate for ToxCast chemical uptake in beans, the edible food product.

Metabolic and Microbiome Alterations Following the Enrichment of a High-Fat Diet With High Oleic Acid Peanuts Versus the Traditional Peanuts Cultivar in Mice

A new Israeli-developed peanut cultivar, “Hanoch-Oleic” (HO), uniquely contains enlarged oleic acid contents and was designed to confer additional beneficial effects over the traditional cultivar, “Hanoch” (HN). This work elucidates metabolic changes and microbiota adaptations elicited by HO addition to a high-fat diet (HFD). Male C57BL/6 mice were fed for 18 weeks with a normal diet or a HFD with/without the addition of HN (HFDh) or HO (HFDo). Body-weight did not differ between HFD-fed mice groups, while liver and adipose weight were elevated in the HFDh and HFD groups, respectively. Insulin-sensitivity (IS) was also decreased in these groups, though to a much greater extent in the traditional peanuts-fed group. Modifications in lipids metabolism were evident by the addition of peanuts to a HFD. Liver inflammation seems to return to normal only in HFDh. Peanuts promoted an increase in α-diversity, with HFDo exhibiting changes in the abundance of microbiota that is primarily associated with ameliorated gut health and barrier capacity. In conclusion, the HO cultivar appears to be metabolically superior to the traditional peanut cultivar and was associated with an improved inflammatory state and microbial profile. Nevertheless, IS-negative effects reinforced by peanuts addition, predominantly NH, need to be comprehensively defined.

The Rhizosphere Microbiomes of Five Species of Coffee Trees

Coffee is one of the most important commodities in the global market. Of the 130 species of Coffea, only Coffea arabica and Coffea canephora are actually cultivated on a large scale. Despite the economic and social importance of coffee, little research has been done on the coffee tree microbiome. To assess the structure and function of the rhizosphere microbiome, we performed a deep shotgun metagenomic sequencing of the rhizospheres of five different species, C. arabica, C. canephora, Coffea stenophylla, Coffea racemosa, and Coffea liberica. Our findings indicated that C. arabica and C. stenophylla have different microbiomes, while no differences were detected between the other Coffea species. The core rhizosphere microbiome comprises genera such as Streptomyces, Mycobacterium, Bradyrhizobium, Burkholderia, Sphingomonas, Penicillium, Trichoderma, and Rhizophagus, several of which are potential plant-beneficial microbes. Streptomyces and mycorrhizal fungi dominate the microbial communities. The concentration of sucrose in the rhizosphere seems to influence fungal communities, and the concentration of caffeine/theobromine has little effect on the microbiome. We also detected a possible relationship between drought tolerance in Coffea and known growth-promoting microorganisms. The results provide important information to guide future studies of the coffee tree microbiome to improve plant production and health.

IMPORTANCE The microbiome has been identified as a fundamental factor for the maintenance of plant health, helping plants to fight diseases and the deleterious effects of abiotic stresses. Despite this, in-depth studies of the microbiome have been limited to a few species, generally with a short life cycle, and perennial species have mostly been neglected. The coffee tree microbiome, on the other hand, has gained interest in recent years as Coffea trees are perennial tropical species of enormous importance, especially for developing countries. A better understanding of the microorganisms associated with coffee trees can help to mitigate the deleterious effects of climate change on the crop, improving plant health and making the system more sustainable.

Irrigation of soil with reclaimed wastewater acts as a buffer of microbial taxonomic and functional biodiversity

The usage of reclaimed wastewater (RWW) for irrigation of agricultural soils is increasingly being acknowledged for reducing water consumption by promoting reuse of treated wastewater, and for the delivery of extant nutrients in the soil. The downside is that RWW may be a vector for contamination of soils with contaminants of emerging concern (CECs), if left uncontrolled. Its usage is anticipated to alter the soil properties, consequently also the soil microbial community. In the present study, soil microcosms were set to monitor how short periods (up to fourteen days) of RWW irrigation influence the soil ecosystem, namely its physicochemical properties, functioning, and colonising microbiota (differentiating fungi from bacteria). Two scenarios were studied: clean soil and soil contaminated (spiked) with 9 CECs, at conditions that limit any abiotic decay processes, monitoring along time fluctuations in the taxonomic and functional microbiota diversity. As shortly as fourteen days, the irrigation of either soil with RWW did not significantly (p > 0.05) alter its physicochemical properties and scarcely impacted the bioremediation processes of the CECs that showed decay levels ranging from 24% to 100%. Bacillus spp. dominance was enhanced along time in all the soil microcosms (reaching over 70% of the total abundance on the 7th day) but the RWW help to preserve, to some extent, high bacterial diversity. Besides, irrigation with RWW acted as a buffer of the soil mycobiota, limiting alterations in its composition caused either along time (to a minor degree) or due to contamination with CECs (to a great degree). This includes limiting the rise of Rhizopus sp. relative abundance. Collectively, our data support the utility of short-term periods of RWW irrigation for preserving the soil microbial diversity and functioning, especially when fungi are considered.

The role of soils in regulation of freshwater and coastal water quality

Water quality regulation is an important ecosystem service function of soil. In this study, the mechanism by which soil regulates water quality was reviewed, and the effects of soil management on water quality were explored. A scientometrics analysis was also conducted to explore the research fields and hotspots of water quality regulation of soil in the past 5 years. This review found that the pollutants entering the soil can be mitigated by precipitation, adsorption and desorption, ion exchange, redox and metabolic decomposition. As an optimal substrate, soil in constructed wetlands has perfect performance in the adsorption and passivation of pollutants such as nitrogen, phosphorus and heavy metals in water, and degradation of pesticides and emerging contaminants. Mangrove wetlands play an important role in coastal zone protection and coastal water quality restoration. However, the excessive application of agricultural chemicals causes soil overload, which leads to the occurrence of agricultural non-point source pollution. Under the dual pressures of climate change and food insecurity in the future, developing environmentally friendly and economically feasible sustainable soil management measures is crucial for maintaining the water purification function of soil by relying on the accurate quantification of soil function based on big data and modelling. This article is part of the theme issue 'The role of soils in delivering Nature's Contributions to People'.

Plant and soil microbial community responses to different water management strategies in an almond crop

Climate change is one of the main challenges facing the agricultural sector as it strives to meet global food needs. In arid and semiarid areas, the scarcity of water imposes the use of alternative sources - such as reclaimed water (RW) or desalinated water (DW) - and of deficit irrigation strategies, such as regulated deficit irrigation (RDI), in order to maintain productivity. The impact of both alternative water sources and RDI strategies on soil microbial communities in conjunction with the crop response has been little studied, and far less in fruit trees. Here, we evaluated the effects of the irrigation water quantity (RDI or the optimal water amount) and quality (DW or saline RW) on: i) the biomass, composition, and activity of the soil microbial community, and ii) the plant agro-physiological response at the level of the water status, nutrients, vegetative growth, and yield of almond trees. The DW-RDI treatment had a lower vegetative growth than the rest, reducing the nutrient requirements and increasing the contents of organic carbon and nitrogen in soil. This coincided with a significant increase in the bacterial biomass and enzyme activities in soil, as well as with a decrease in plant nutrient use efficiencies and yield. Irrigation with RW increased the fungal biomass. When there were no water restrictions (RW-FI), none of the plant agro-physiological parameters were affected; when RDI was applied (RW-RDI), the highest soil sodicity was reached and vegetative growth and yield were negatively affected, although the plant nutrient use efficiencies did not decrease as much as with DW-RDI. In addition, the plant nutrient use efficiencies were negatively correlated with the soil enzyme activities. These results improve our knowledge of the functioning of plant-soil interactions in Mediterranean crops subjected to different irrigation strategies.

Virome studies of food production systems: time for 'farm to fork' analyses

The food industry is under increasing pressure to produce high quality, traceable and minimally processed foods that are produced using sustainable approaches and ingredients. In line with the latter, there is an increased pressure for plant-based products to replace animal-derived products. Until recently, research efforts have mainly focused on dairy and meat products owing to their economic importance. The shift towards plant-based diets and food production requires a corresponding shift in research efforts to define the microbial requirements for and composition of (novel) plant-based foods, the (micro)organisms that are beneficial to such production systems, and the abundance and role of (bacterio)phages in shaping the microbial landscape of these foods. In this review, we explore current efforts in the area of virome analysis of foods and food production environments and highlight the need for more unified approaches to understand the contribution of phages in food safety and quality, and to develop novel tools to enhance the traceability of foods.

Carryover effects minimized the positive effects of treated wastewater on anuran development

Constructed wetlands (CWs) are a potential solution for wastewater treatment due to their capacity to support native species and provide tertiary wastewater treatment. However, CWs can expose wildlife communities to excess nutrients and harmful contaminants, affecting their development, morphology, and behavior. To examine how wastewater CWs may affect wildlife, we raised Southern leopard frogs, Lithobates sphenocephalus, in wastewater from conventional secondary lagoon and tertiary CW treatments for comparison with pondwater along with the presence and absence of a common plant invader to these systems - common duckweed (Lemna minor) - and monitored their juvenile development for potential carryover effects into the terrestrial environment. The tertiary CW treatment did not change demographic or morphological outcomes relative to conventional wastewater treatment in our study. Individuals emerging from both wastewater treatments demonstrated lower terrestrial survival rates than those emerging from pondwater throughout the experiment though experiment-wide survival rates were equivalent among treatments. Individuals from wastewater treatments transformed at larger sizes relative to those in pondwater, but this advantage was minimized in the terrestrial environment. Individuals that developed with duckweed had consistent but marginally better performance in both environments. Our results suggest a potential trade-off between short-term benefits of development in treated effluent and long-term consequences on overall fitness. Overall, we demonstrate that CWs for the purpose of wastewater treatment may not be suitable replicates for wildlife habitat and could have consequences for local population dynamics.

Insights into the effects of heavy metal pressure driven by long-term treated wastewater irrigation on bacterial communities and nitrogen-transforming genes along vertical soil profiles

Irrigation with treated wastewater (TWW) influences soil ecological function due to the accumulation of heavy metals (HMs) and nutrients in soils. However, the interaction between HMs and microbial processes in TWW-irrigated soil has not been fully explored. We investigated the effect of HMs on bacterial communities and nitrogen-transforming (N-transforming) genes along vertical soil profiles irrigated with domestic TWW (DTWW) and industrial TWW (ITWW) for more than 30 years. Results indicate that long-term TWW irrigation reshaped bacterial community structure and composition. Irrigation with ITWW led to increased accumulation of Cd, Cr, Cu, Pb, Zn, and Ni in soils than DTWW. Accumulation of inorganic N, soil organic carbon, and HMs in topsoil irrigated with ITWW contributed to the activities of Micrococcaceae. The effect of the activation of nutrient factors on Bacillus, which was the dominant species in DTWW-irrigated soils, was greater than that of HMs. HM pressure driven by ITWW irrigation changed the vertical distribution of N-transforming functional genes, increasing the abundance of amoA gene and decreasing that of nifH through soil depth. ITWW irrigation enhanced the denitrification capacity in topsoil; ammonia-oxidizing capacity in deeper soil was increased after long-term irrigation with DTWW and ITWW, suggesting a potential risk of nitrogen loss.

Soil salinization management for sustainable development: A review

The expansion of irrigated agriculture is of paramount importance to feed the burgeoning global population. However, without proper management, this expansion can result in environmental problems of irrigation-induced soil salinization. A recent FAO estimate reported that a large portion of total global soil resources are degraded and this problem is persistently expanding. Many irrigated areas of the world are facing the twin problems of soil salinization and waterlogging and presently over 20% of the total global irrigated area is negatively affected by these problems. And, if left unattended, this problem could expand to over 50% of the total global irrigated areas by 2050. The proper management of the aforementioned soil salinization is imperative for achieving most of the Sustainable Development Goals (SDGs) of the United Nations. For example, soil salinization management is vital for achieving the 'Zero Hunger' (SDG2) and 'Life on Land' (SDG15) among other SDGs. This paper provides a comprehensive review of different measures used for managing the environmental problems of soil salinization. All the possible sources of related and up to date literature have been accessed and over 250 publications were collected and thoroughly analyzed for this review. The centrality of the environmental problems is provided. The background of the problems, managing rising water table to control soil salinization, the role of drainage frameworks, the conjunctive use of diverse water sources, utilization of numerical models, and the use of remote sensing and GIS systems are described. And the application of the aforementioned techniques and methods in various case study regions across the globe are discussed which is followed by discussion and research gaps. Derived from the literature analysis and based on the identified research gaps, some key recommendations for future research have been made which could be useful for the stakeholders. The literature analysis revealed that an all-inclusive approach for dealing with the aforesaid environmental problems has been barely considered in the previous studies. Similarly, the continuing impacts of growing salt-tolerant plants on soil characteristics and the environment in total have not been widely considered in the previous investigations. Likewise, better irrigation practices and improved cropping systems along with the long-term environmental impacts of a particular approach has not been extensively covered in these studies. Also, previous studies have scarcely incorporated economic, social, and environmental aspects of the salinization problem altogether in their analysis. The analysis suggested that an inclusive feedback-supported simulation model for managing soil salinization should be considered in future research as the existing models scarcely considered some vital aspects of the problem. It is also suggested to enhance the sensing methods besides retrieval systems to facilitate direct detection of salinization and waterlogging parameters at large-scales. The existing time-lag between occurrence and recording of various data is also suggested to improve in the future scenario by the usage of information from multiple satellites that lessens the problems of spatial resolution by increasing the system efficiency.

Elucidating the Diversity and Potential Function of Nonribosomal Peptide and Polyketide Biosynthetic Gene Clusters in the Root Microbiome

Polyketides (PKs) and nonribosomal peptides (NRPs) are two microbial secondary metabolite (SM) families known for their variety of functions, including antimicrobials, siderophores, and others. Despite their involvement in bacterium-bacterium and bacterium-plant interactions, root-associated SMs are largely unexplored due to the limited cultivability of bacteria. Here, we analyzed the diversity and expression of SM-encoding biosynthetic gene clusters (BGCs) in root microbiomes by culture-independent amplicon sequencing, shotgun metagenomics, and metatranscriptomics. Roots (tomato and lettuce) harbored distinct compositions of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) relative to the adjacent bulk soil, and specific BGC markers were both enriched and highly expressed in the root microbiomes. While several of the highly abundant and expressed sequences were remotely associated with known BGCs, the low similarity to characterized genes suggests their potential novelty. Low-similarity genes were screened against a large set of soil-derived cosmid libraries, from which five whole BGCs of unknown function were retrieved. Three clusters were taxonomically affiliated with Actinobacteria, while the remaining were not associated with known bacteria. One Streptomyces-derived BGC was predicted to encode a polyene with potential antifungal activity, while the others were too novel to predict chemical structure. Screening against a suite of metagenomic data sets revealed higher abundances of retrieved clusters in roots and soil samples. In contrast, they were almost completely absent in aquatic and gut environments, supporting the notion that they might play an important role in root ecosystems. Overall, our results indicate that root microbiomes harbor a specific assemblage of undiscovered SMs.IMPORTANCE We identified distinct secondary-metabolite-encoding genes that are enriched (relative to adjacent bulk soil) and expressed in root ecosystems yet almost completely absent in human gut and aquatic environments. Several of the genes were distantly related to genes encoding antimicrobials and siderophores, and their high sequence variability relative to known sequences suggests that they may encode novel metabolites and may have unique ecological functions. This study demonstrates that plant roots harbor a diverse array of unique secondary-metabolite-encoding genes that are highly enriched and expressed in the root ecosystem. The secondary metabolites encoded by these genes might assist the bacteria that produce them in colonization and persistence in the root environment. To explore this hypothesis, future investigations should assess their potential role in interbacterial and bacterium-plant interactions.

Unveiling dynamics of size-dependent antibiotic resistome associated with microbial communities in full-scale wastewater treatment plants

Serious concerns have been raised regarding antibiotic resistance genes (ARGs) with respect to their potential threat to human health. Wastewater treatment plants (WWTPs) have been considered to be hotspots for ARGs. In this study, high-throughput quantitative polymerase chain reaction (HT-qPCR) was used to profile size-dependent ARGs and mobile genetic elements (MGEs) divided by particle-associated (PA) assemblages (>3.0-μm), free-living (FL) bacteria (0.2 - 3.0-μm) and cell-free (CF) DNA (< 0.2-μm) in two full-scale WWTPs (plants A and B) and a receiving stream. The results revealed that FL-ARGs were predominant in WWTPs and the receiving stream, especially in the final effluent of both plants. More than 40 types of CF-ARGs and CF-MGEs were detected with absolute abundances ranging from 6.0 ± 0.7 × 10⁵ to 1.0 ± 0.2 × 10⁸ copies/mL in wastewater, and relatively high abundances were also detected in the final effluent of the two plants, suggesting that CF-ARGs were important sources spreading from the WWTPs to the receiving environment. Plant A exhibited higher log-removal of size-fractionated ARGs and MGEs than was observed for plant B, which was attributed to the enhanced settleability of PA assemblages and FL bacteria by additional macrophytes and chemical coagulants. Ultraviolet disinfection had limited effects on ARGs and MGEs of the PA and FL fractions, which was probably ascribed to the protective matrices of the particles and cell walls. The bacterial communities of the two plants were significantly different among the size fractions (p < 0.01). The variation partitioning analysis (VPA) indicated that the microbial community structures and MGEs contributed a variation of 68.2% in total to the relative abundance changes of size-fractionated ARGs. Procrustes analyses and Mantel tests showed that the relative abundances of ARGs were significantly correlated with bacterial community structures. These results suggested that the bacterial community structures and MGEs might have been the main drivers of the size-fractionated ARG disseminations. This study provides novel insights into size-fractionated ARGs and MGEs in full-scale WWTPs and may lead to the identification of key targets to control the spread of ARGs.

Effects of prescription antibiotics on soil- and root-associated microbiomes and resistomes in an agricultural context

The use of treated wastewater for crop irrigation is rapidly increasing to respond to the ever-growing demands for water and food resources. However, this practice may contribute to the spread of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) in agricultural settings. To evaluate this potential risk, we analyzed microbiomes and resistomes of soil and Lactuca sativa L. (lettuce) root samples from pots irrigated with tap water spiked with 0, 20, or 100 μg L^-1 of a mixture of three antibiotics (Trimethoprim, Ofloxacin, Sulfamethoxazole). The presence of antibiotics induced changes in bacterial populations, particularly in soil, as revealed by 16S rDNA sequence analysis. Parallel shotgun sequencing identified a total of 56 different ARGs conferring resistance against 14 antibiotic families. Antibiotic -treated samples showed increased loads of ARGs implicated in mutidrug resistance or in both direct and indirect acquired resistance. These changes correlated with the prevalence of Xantomonadales species in the root microbiomes. We interpret these data as indicating different strategies of soil and root microbiomes to cope with the presence of antibiotics, and as a warning that their presence may increase the loads of ARBs and ARGs in edible plant parts, therefore constituting a potential risk for human consumers.

Mercury in rice paddy fields and how does some agricultural activities affect the translocation and transformation of mercury - A critical review

Human exposure to methylmercury (MeHg) through rice consumption is raising health concerns. It has long been recognized that MeHg found in rice grain predominately originated from paddy soil. Anaerobic conditions in paddy fields promote Hg methylation, potentially leading to high MeHg concentrations in rice grain. Understanding the transformation and migration of Hg in the rice paddy system, as well as the effects of farming activities, are keys to assessing risks and developing potential mitigation strategies. Therefore, this review examines the current state of knowledge on: 1) sources of Hg in paddy fields; 2) how MeHg and inorganic Hg (IHg) are transformed (including abiotic and biotic processes); 3) how IHg and MeHg enter and translocate in rice plants; and 4) how regular farming activities (including the application of fertilizer, cultivation methods, choice of cultivar), affect Hg cycling in the paddy field system. Current issues and controversies on Hg transformation and migration in the paddy field system are also discussed.

Comparative Study on Soil Microbial Diversity and Structure Under Wastewater and Groundwater Irrigation Conditions

Wastewater (WW) irrigation to agricultural soils is one of the most economical and effective water-saving strategies. The effects of WW irrigation on soil microbial communities have gained increasing focus as these effects are not well understood. In this study, the effects of WW and groundwater (GW) irrigation on microbial diversity and structure were compared using the high-throughput sequencing analysis of 16S rDNA amplicons. Soil samples irrigated by WW for several decades and maize soil (loamy) samples irrigated by GW were collected from Luancheng Town, Shijiazhuang City, China. Compared to the GW groups, WW groups exhibited non-significant soil bacterial community abundance at the 0-20 and 20-40 cm depths. WW irrigation significantly altered the bacterial community composition and structures compared to GW irrigation. The relative abundance of Proteobacteria and Firmicutes increased in WW irrigated soil, while Actinobacteria decreased. Moreover, 14 significantly abundant biomarkers from Proteobacteria and Firmicutes that corresponded with WW irrigation were identified. Additionally, WW irrigation enriched some KEGG pathways that corresponded with metabolism and human diseases. The physical and chemical properties of WW irrigated soil may shape the compositions and structures of soil bacterial communities. The findings of this study illuminated the effects of wastewater irrigation on microbial characteristics, which is important for estimating the effects of long-term wastewater irrigation on soil environmental health.

The microbiome as a biosensor: functional profiles elucidate hidden stress in hosts

BACKGROUND

Microbial communities are highly responsive to environmental cues, and both their structure and activity can be altered in response to changing conditions. We hypothesized that host-associated microbial communities, particularly those colonizing host surfaces, can serve as in situ sensors to reveal environmental conditions experienced by both microorganisms and the host. For a proof-of-concept, we studied a model plant-soil system and employed a non-deterministic gene-centric approach. A holistic analysis was performed using plants of two species and irrigation with water of low quality to induce host stress. Our analyses examined the genetic potential (DNA) and gene expression patterns (RNA) of plant-associated microbial communities, as well as transcriptional profiling of host plants.

RESULTS

Transcriptional analysis of plants irrigated with treated wastewater revealed significant enrichment of general stress-associated root transcripts relative to plants irrigated with fresh water. Metagenomic analysis of root-associated microbial communities in treated wastewater-irrigated plants, however, revealed enrichment of more specific stress-associated genes relating to high levels of salt, high pH and lower levels of oxygen. Meta-analysis of these differentially abundant genes obtained from other metagenome studies, provided evidence of the link between environmental factors such as pH and oxygen and these genes. Analysis of microbial transcriptional response demonstrated that enriched gene content was actively expressed, which implies contemporary response to elevated levels of pH and salt.

CONCLUSIONS

We demonstrate here that microbial profiling can elucidate stress signals that cannot be observed even through interrogation of host transcriptome, leading to an alternate mechanism for evaluating in situ conditions experienced by host organisms. This study is a proof-of-concept for the use of microbial communities as microsensors, with great potential for interrogation of a wide range of host systems. Video Abstract.

Dynamics of soil organic carbon in Typic Torripsamment soils irrigated with raw effluent sewage water

The current research aimed at collecting detailed information about the consequences of cropping history on the accumulation of soil organic carbon (SOC) within different soil depths, i.e., 0-10, 10-20, 20-30 and 30-60 cm. The study site is located at El Gabal El Asfar area (Egypt) whose soils were irrigated with raw sewage effluent as a sole source of irrigation for different periods extended up to 80 years. SOC increased progressively with increasing cropping time, and on the other hand, decreased noticeably with increasing soil depth. The increases significantly correlated with both of the silt and clay contents in soils which increased with time. Soil bulk density and the hydraulic conductivity significantly and negatively correlated with SOC, respectively. Fractions of SOC, i.e., water soluble C, hot water C and soil biomass C in the surface soil layer (0-10 cm), increased progressively with increasing time of land use. Such pools significantly correlated with SOC on one hand and with each other on the other hand. Active (labile) organic carbon fraction increased with time. This fraction also significantly correlated with the different C pools. In conclusion, the hypothesis that SOC is physically protected against soil microbes within the soil requires more investigations to clarify such results obtained herein because this study highlighted the presence of a dynamic equilibrium among the different fractions or pools of the SOC.

Antibiotic resistance and class 1 integron gene dynamics along effluent, reclaimed wastewater irrigated soil, crop continua: elucidating potential risks and ecological constraints

Reuse of municipal wastewater is a growing global trend, but currently there is lack of consensus regarding the potential dissemination of antibiotic resistance elements by treated wastewater irrigation. We tracked intI1, a proxy for anthropogenic pollution, and an assemblage of antibiotic resistance genes associated with mobile elements and/or wastewater (bla_GES, bla_OXA2, bla_OXA10, bla_TEM, bla_CTX-M-32 and qnrS) in treated wastewater effluents, effluent stabilization reservoirs, and along irrigation water-soil-crop continua in experimental lysimeters and large-scale commercial fields. While several of the targeted antibiotic resistance genes were profuse in effluents, there was almost no correlation between gene abundance in irrigation water and those detected in soil, and no evidence of systematic gene transfer to irrigated soil or crops. In contrast, soil intI1 abundance correlated strongly to irrigation water levels in lysimeters and sandy field soils, but this was not the case for clay-rich soils or for most of the analyzed crops, suggesting that intI1 may not always be a reliable marker for tracking the impact of treated wastewater irrigation. We hypothesize that "ecological boundaries" expedited by biotic and abiotic factors constrain dissemination of antibiotic resistance elements, and assert that a more holistic perception of these factors is crucial for understanding and managing antibiotic resistance dissemination.

Linking the response of soil microbial community structure in soils to long-term wastewater irrigation and soil depth

Irrigation with treated wastewater (TWW) has become a prevailing agricultural practice due to the scarcity of fresh water resources, which may have a significant impact on the microbial communities that are critical to many biogeochemical processes in soils. However, it is unclear whether there are links between soil microbial responses to long-term irrigation with different sources of wastewater and soil depth. Here we assess the influence of treated domestic (DTWW), leather industry (LTWW) and pharmaceutical (PTWW) wastewater on microbial communities in vertical soil profiles using high-throughput sequencing based on 16S rRNA and internal transcribed spacer (ITS) gene profiling. We found that microbial α-diversity in the vertical profiles of soils was significantly influenced by TWW irrigation. Bacteria and fungi in different soil depths showed distinct responses to TWW; irrigation with TWW markedly increased abundance of bacterial OTUs and inhibited abundance of fungal OTUs. β-diversity analysis showed that the effect of TWW irrigation on microbial communities was greater than the effect of soil depth, and microbes in subsurface soil were more sensitive to different sources of irrigation water. We also found that, based on β-diversity analysis, irrigation with treated industrial wastewater, including LTWW and PTWW, had a greater impact on microbial community structures than DTWW. TWW irrigation significantly affected the composition of indigenous soil microbial communities at different depths and might introduce exogenous microbes into the soil environment. Our work explicitly demonstrates the vertical responses of bacterial and fungal communities in soils to irrigation with TWW from different sources, which can provides insights into the microbial-dominated geochemical processes from the perspective of the entire soil profile under the context of wastewater irrigation.

Distribution of antibiotic resistance genes in soils and crops. A field study in legume plants (Vicia faba L.) grown under different watering regimes

Social concern has raised during the last years due to the development of antibiotic resistance hotspots in different environmental compartments, including the edible parts of crops. To assess the influence of the water quality used for watering, we collected samples from soil, roots, leaves and beans from the legume plant Vicia faba (broad beans) in three agricultural peri-urban plots (Barcelona, NE Spain), irrigated with either groundwater, river water, or reclaimed water. Antibiotic resistance genes (ARGs) sul1, tetM, qnrS1, bla_CTX-M-32,bla_OXA-58, mecA, and bla_TEM were quantified by real-time PCR, along with 16S rDNA and intl1 sequences, as proxies for bacterial abundance and integron prevalence, respectively. Microbiome composition of all samples were analyzed by high-throughput DNA sequencing. Results show a gradient of bacterial species diversity and of ARG prevalence from highly diverse soil samples to microbially-poor beans and leaves, in which Rhizobiales essentially displaced all other groups, and that presented very small loads of ARGs and integron sequences. The data suggest that the microbiome and the associated resistome were likely influenced by agricultural practices and water quality, and that future irrigation water legal standards should consider the specific Physiology of the different crop plants.